Yes, you have more people in the population centers. They're generally a very homogenous group by political thought, and vote almost as a left wing bloc in most cases. You're simply arguing that the left should be more powerful than it is. Nobody cries about the electoral college until a Republican wins. Nobody cries about representation when the left is in power.
There are things that are wrong in the US political system, but the electoral college and the house representation aren't those things. They're the best of the bad solutions to keeping away from a tyranny.
And also, the majority of this country votes democrat in every election since 2000, but because of gerrymandering the house retains a Republican majority. If the house matched the breakdown of national popular votes for house reps, it would be significantly Democrat.
You're using a tiny fraction of history to discuss this, and even within that tiny fraction your numbers are incorrect as the the dems held the majority from 2007 to 2011 and only lost it in the backlash from the health care debacle.
Also the national popular vote is totally irrelevant to the house membership. It's not set up that way.